Microarray gene expression data quality control.

<p>A: the number of genes detected at p-value < 0.05 (red line) and p-value < 0.01 (blue line). Detection p-value is a measurement of confidence that a given transcript is expressed above the background level. B: Sample quality assessment by comparison of 95^th signal intensity values (red line) and signal-to-noise ratio (blue line) across samples. Signal-to-noise ratio is calculated as a ration of 95^th and 5^th percentile (p95/p05) in non-normalized data. C: Hierarchical clustering of samples after normalization and averaging of biological replicates.</p

Neural and dopaminergic differentiation.

<p>A-B: Immunocytochemistry in <i>SNCA</i> triplication (A6) NSCs with antibodies against NSC markers SOX1, NESTIN, and PAX6. C-D: Immunocytochemistry for dopaminergic (TH and LMX1A), and midbrain (FOXA2) markers. Scale bar as marked.</p

Pluripotency verification of PD patient iPSC.

<p>A: Pluripotency score for iPSC lines A6, B119, I3, K20, P1, S110, T101,L1 and Y09. ESC H9 line served as a positive control, whereas fibroblasts from the healthy subject (Y line) were used as a negative control. Pluripotency range is depicted in red, whereas non-pluripotent range is shown in blue. B: Novelty score for tested samples. Low novelty score (green bars) is characteristic for pluripotent cell lines, whereas high novelty sore (red) highlights sample that deviated from the pluripotent transcriptional signature. C: Hierarchical clustering of all samples. D: Combination of pluripotency and novelty scores illustrates that iPSC and ESC samples are grouped together (red background—high pluripotency and low novelty scores). Y fibroblast line had the opposite result (blue background—low pluripotency and high novelty scores).</p

Integration-free iPSC lines generated from PD patient and control fibroblasts.

<p>Integration-free iPSC lines generated from PD patient and control fibroblasts.</p

Genes up or down regulated 3 fold in control and <i>SNCA</i> triplication dopaminergic cultures after MPP treatment.

<p>Genes up or down regulated 3 fold in control and <i>SNCA</i> triplication dopaminergic cultures after MPP treatment.</p

Genes up or down regulated in all PD-patient specific dopaminergic cultures relative to control.

<p>Genes up or down regulated in all PD-patient specific dopaminergic cultures relative to control.</p

Mitogenic genes up or down regulated 3 fold in <i>SNCA</i> triplication dopaminergic cultures relative to control.

<p>Mitogenic genes up or down regulated 3 fold in <i>SNCA</i> triplication dopaminergic cultures relative to control.</p

Gene up or down regulated in <i>SNCA</i> triplication dopaminergic cultures relative to healthy control.

<p>Gene up or down regulated in <i>SNCA</i> triplication dopaminergic cultures relative to healthy control.</p

Additional file 1 of An expanded evaluation of protein function prediction methods shows an improvement in accuracy

A document containing a subset of CAFA2 analyses that are equivalent to those provided about the CAFA1 experiment in the CAFA1 supplement. (PDF 11100 kb